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  1. Jalview
  2. JAL-2898

stop_gained variants not shown correctly on peptide sequence

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    Details

    • Type: New Feature
    • Status: Closed
    • Priority: Minor
    • Resolution: Fixed
    • Affects Version/s: 2.10.3
    • Fix Version/s: 2.11.0
    • Component/s: sequencefeatures
    • Labels:
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      Description

      Fetch the Ensembl example, Get Cross-References | Uniprot, and navigate to the variant at column 178 (position 163 of ENSP00000288602).
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      p.Arg163Gln
      p.Arg163Leu
      p.Arg163null
      The last of these is for a codon variant (CGA -> TGA) which is a premature stop. It should be shown as a variant of type 'stop_gained' (or perhaps 'polypeptide_truncation'?) on the protein sequence.

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        1. StopLostVariant.jpg
          76 kB
          Mungo Carstairs
        2. StopVariant.jpg
          65 kB
          Mungo Carstairs

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              Assignee:
              gmungoc Mungo Carstairs
              Reporter:
              gmungoc Mungo Carstairs
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                Created:
                Updated:
                Resolved: